1LTX

Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

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This is version 1.4 of the entry. See complete history


Literature

Structure of Rab Escort Protein-1 in Complex with Rab Geranylgeranyltransferase

Pylypenko, O.Rak, A.Reents, R.Niculae, A.Sidorovitch, V.Cioaca, M.D.Bessolitsyna, E.Thoma, N.H.Waldmann, H.Schlichting, I.Goody, R.S.Alexandrov, K.

(2003) Mol Cell 11: 483-494

  • DOI: 10.1016/s1097-2765(03)00044-3
  • Primary Citation of Related Structures:  
    1LTX

  • PubMed Abstract: 
  • Posttranslational geranylgeranylation of Rab GTPases is catalyzed by Rab geranylgeranyltransferase (RabGGTase), which consists of a catalytic alpha/beta heterodimer and an accessory Rab escort protein (REP). The crystal structure of isoprenoid-bound RabGGTase complexed to REP-1 has been solved to 2 ...

    Posttranslational geranylgeranylation of Rab GTPases is catalyzed by Rab geranylgeranyltransferase (RabGGTase), which consists of a catalytic alpha/beta heterodimer and an accessory Rab escort protein (REP). The crystal structure of isoprenoid-bound RabGGTase complexed to REP-1 has been solved to 2.7 A resolution. The complex interface buries a surprisingly small surface area of ca. 680 A and is unexpectedly formed by helices 8, 10, and 12 of the RabGGTase alpha subunit and helices D and E of REP-1. We demonstrate that the affinity of RabGGTase for REP-1 is allosterically regulated by phosphoisoprenoid via a long-range trans-domain signal transduction event. Comparing the structure of REP-1 with the closely related RabGDI, we conclude that the specificity of the REP:RabGGTase interaction is defined by differently positioned phenylalanine residues conserved in the REP and GDI subfamilies.


    Related Citations: 
    • Crystallization and Preliminary X-ray Diffraction Analysis of the Rab Escort Protein-1 in Complex with Rab Geranylgeranyltransferase
      Rak, A., Reents, R., Pylypenko, O., Niculae, A., Sidorovitch, V., Thoma, N.H., Waldmann, H., Schlichting, I., Goody, R.S., Alexandrov, K.
      (2001) J Struct Biol 136: 158

    Organizational Affiliation

    Department of Biomolecular Mechanisms, Max-Planck-Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNITA567Rattus norvegicusMutation(s): 0 
Gene Names: RabggtaGgta
EC: 2.5.1 (PDB Primary Data), 2.5.1.60 (UniProt)
UniProt
Find proteins for Q08602 (Rattus norvegicus)
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08602
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RAB GERANYLGERANYLTRANSFERASE BETA SUBUNITB331Rattus norvegicusMutation(s): 0 
Gene Names: RabggtbGgtb
EC: 2.5.1 (PDB Primary Data), 2.5.1.60 (UniProt)
UniProt
Find proteins for Q08603 (Rattus norvegicus)
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UniProt GroupQ08603
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Rab Escort Protein 1C [auth R]650Rattus norvegicusMutation(s): 3 
Gene Names: ChmRep1
UniProt
Find proteins for P37727 (Rattus norvegicus)
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UniProt GroupP37727
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
AAAAD [auth P]4N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAR
Query on FAR

Download Ideal Coordinates CCD File 
G [auth P]FARNESYL
C15 H26
JXBSHSBNOVLGHF-BUJBXKITSA-N
 Ligand Interaction
ZN
Query on ZN

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E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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F [auth R]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.7α = 90
b = 197.3β = 112.8
c = 85.3γ = 90
Software Package:
Software NamePurpose
ProDCdata collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-21
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations